Abstract: Functional protein microarrays find applications in high throughput disease biomarker discovery, understanding the incidence and role of post translational modifications (PTMs) in disease pathology, investigating activity and function of enzymes, protein?protein and protein? small molecule interactions, among others. Nucleic Acid Programmable Protein Array (NAPPA) technology is a robust method for producing cell-free in situ expressed functional protein microarrays in human lysate, freshly expressed and displayed at the time of assay, and has been widely applied in disease biomarker discovery research over the last decade. We aim to develop an advanced instrument for automating the production of NAPPA IPC (Isolated Protein Capture) high density protein microarrays on glass slides. Once the instrument is developed, we expect similar improvements in simplicity, speed and quality of NAPPA protein microarray assays as was seen when DNA microarrays were transferred from manual to automated workstations. In addition to clinical biomarker research, it is an ideal platform for profiling for disease biomarkers in animal models, a subset of which can then be monitored as prognostic biomarkers, indicators of end points in drug development pre-clinical trials.